[Refactor] LinkML Schema Service: Update OpenAPI Adjustment Script to treat schema like YAML

[infispiel]

Description

Taken from #1856

In order to use an OpenAPI Schema with Connexion (which is used for this particular microservice implementation), certain adjustments to the schema must be made. Specifically, the attributes operationId and x-openapi-router-controller must be present to help Connexion identify what python functions to call on request.

A script was made to take an OpenApi schema and add these attributes (helpers/SchemaAdapter), but currently it does this by operating on the schema like plaintext. This should be adjusted to properly load the schema as Yaml and add these attributes to the parsed Yaml, for stability reasons.